Journal Club Discussions

Every other week we will have a Journal Club wherein we discuss a paper in small group formats.

There will also be a sheet of Study Questions posted on Wikispaces - that you are to complete before class and turn in.

You are required to PRINT OUT the paper and the Study Q's and BRING them to class with you! (bringing it on your laptop or phone does not count!)

• bringing the paper with you is part of your grade
• you are welcome to print these papers in the Painter Lab (please do 2 pages per sheet to conserve paper)
• Also, while you are at it - be sure to ask a friend if they need a copy printed too!

During the class small group discussion in class, there will be a Question sheet that each group will work on collectively - but each person will turn theirs in for a grade.

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Journal Club Schedule (updated 090512)
1st Week: none
2nd Week: Sept. 5th - none
3rd Week: Sept.12th - 1st Journal Club
4th Week: Sept. 19th - none
5th Week: Sept. 26th - 2nd Journal Club
6th Week: Oct. 3rd - none
7th Week: Oct 10th - 3rd Journal Club
8th Week : Oct. 17th - 4th Journal Club
9th Week: Oct. 24th - NONE - FRI Open House
10th Week: Oct. 31st - 5th Journal Club
11th Week: Nov. 7th - none
12th Week: Nov. 14th - 6th Journal Club
13th Week: Nov 21st - none
14th Week: Nov 28th - 7th Journal Club ??
15th Week: Dec 5th (Last Class)





6th Journal Club - Nov 14th
Paper:
Identification of novel bacterial histidine biosynthesis inhibitors using docking, ensemble rescoring, and whole-cell assays. Henriksen ST, Liu J, Estiu G, Oltvai ZN, Wiest O. Bioorg Med Chem. 2010 Jul 15;18(14):5148-56.
MochalkinVirtualScreeningBiotinCarboxylaseFASII_ACSCHemBiol2009.pdf
Study Q's:
These are not 'take home' questions - we will do these in class as 2 separate teams. But you may want to look over them to see if you are able to answer them in class.
JournalClubQuestions111412_BiotinCarboxy.doc




Some good extra reading for the Springers & Sidestreamers:
Paper:

1. Park, H.; Kim, Y. J.; Hahn, J. S., A novel class of Hsp90 inhibitors isolated by structure-based virtual screening. Bioorganic & Medicinal Chemistry Letters 2007, 17 (22), 6345-6349.
   • Park Hsp90 paper
2. Alanis, A. J., Resistance to antibiotics: are we in the post-antibiotic era? Arch Med Res 2005, 36 (6), 697-705.
   • Alanis paper
3. Zolli-Juran, M.; Cechetto, J. D.; Hartlen, R.; Daigle, D. M.; Brown, E. D., High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate. Bioorganic & Medicinal Chemistry Letters 2003, 13 (15), 2493-2496.
   Zolli-Juran paper

1st Journal Club Fall 2012
Paper:
Kovac, A.; Konc, J.; Vehar, B.; Bostock, J.; Chopra, I.; Janezic, D.; Gobec, S., Discovery of new inhibitors of D-alanine:D-alanine ligase by structure-based virtual screening. J Med Chem 2008, 51 (23), 7442-8.
KovacDalanineDalanineLigaseVirtualScreenJMedChem2008.pdf

Study Q's: answer these and bring paper copy to class JournalClubQuestions091212_DalaDalaLigase_StudyQs.doc


2nd Journal Club
Paper:
Tomlinson, S.; Malmstrom, R.; Watowich, S., New approaches to structure-based discovery of dengue protease inhibitors. Infect Disord Drug Targets 2009, 9 (3), 327-43.
TomlinsonWatowichDengueVirusInfectiousDisordersDrugTargets2009.pdf




3rd Journal Club - Oct. 10th
Paper:
Bai, Y.; Monzingo, A.; Robertus, J., The X-ray structure of ricin A chain with a novel inhibitor. Arch Biochem Biophys 2009, 483 (1), 23-8.
BaiRicinVirtualScreenToxicon2010.pdf

Study Q's:



4th Journal Club - Oct. 17th
Paper:
Ruda, G.; Campbell, G.; Alibu, V.; Barrett, M.; Brenk, R.; Gilbert, I., Virtual fragment screening for novel inhibitors of 6-phosphogluconate dehydrogenase. Bioorg Med Chem 2010, 18 (14), 5056-62.
RudaTBruceiVirtualDock_6phosphgluconateDehydrogenaseBiorgMedChem2010.pdf

Study Q's:



5th Journal Club - Oct 31st
Paper:
A Novel Small-Molecule Inhibitor of the Avian Influenza H5N1 Virus Determined through
Computational Screening against the Neuraminidase. Jianghong An, Davy C. W. Lee, Anna H.Y. Law, Cindy L.H. Yang, Leo L.M. Poon, Allan S.Y. Lau, and
Steven J.M. Jones J. Med. Chem. 2009, 52, 2667–2672
AnAvianFluInhibitorsH5N1_ComputationalScreenJMedChem2009.pdf

Study Q's:
















LEFTOVER FROM SUMMER:
Henriksson, L. M.; Unge, T.; Carlsson, J.; Aqvist, J.; Mowbray, S. L.; Jones, T. A., Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis. J Biol Chem 2007, 282 (27), 19905-16.
HenrikksonMtDXR_JBiolChem2007.pdf


GAPDH paper - ?? for Fall


6th Papers:

Hirayama, K.; Aoki, S.; Nishikawa, K.; Matsumoto, T.; Wada, K., Identification of novel chemical inhibitors for ubiquitin C-terminal hydrolase-L3 by virtual screening. Bioorg Med Chem 2007, 15 (21),
6810-8.
VDS_UBL3_bioorgmedchem2007.pdf

Sacchettini, J.; Rubin, E.; Freundlich, J., Drugs versus bugs: in pursuit of the persistent predator Mycobacterium tuberculosis. Nat Rev Microbiol 2008, 6 (1), 41-52.
SacchettiniTuberculosis_DrugsVsBugsNatRevMicrobiol2008.pdf



5th Papers

Singh, J.; Chuaqui, C.; Boriack-Sjodin, P.; Lee, W.; Pontz, T.; Corbley, M.; Cheung, H.; Arduini, R.; Mead, J.; Newman, M.; Papadatos, J.; Bowes, S.; Josiah, S.; Ling, L., Successful shape-based virtual screening: the discovery of a potent inhibitor of the type I TGFbeta receptor kinase (TbetaRI). Bioorg Med Chem Lett 2003, 13 (24), 4355-9.
SinghVirtualTGFbetaBioorgMedChemLett2003.pdf





4th Papers

Mochalkin, I.; Miller, J.; Narasimhan, L.; Thanabal, V.; Erdman, P.; Cox, P.; Prasad, J.; Lightle, S.; Huband, M.; Stover, C., Discovery of antibacterial biotin carboxylase inhibitors by virtual screening and fragment-based approaches. ACS Chem Biol 2009, 4 (6), 473-83.
MochalkinVirtualScreeningBiotinCarboxylaseFASII_ACSCHemBiol2009.pdf



OLD:

Journal Club Presentations

Guidelines:

• prepare a 10 minute powerpoint slide show
• [[#|Start]] out with a title slide that has the Journal Article name and Authors on it.
  • Put YOUR name on title slide also since you are presenting.
  • Put the date of the presentation on their as well - and something like 'VDS Summer Journal Club'
• Create an introduction that provides a broad perspective for the specific [[#|work]] being presented. For example, if you are presenting a [[#|paper]] on a new protein, you should provide some background on the protein family and what it does. Don't assume that everyone in your audience knows the background. You can use your own content if you like - along with that given by the authors.
  • Include a picture or image that helps give a visual for the background.
  • Include any statistics about the disease and its prevalence (this is motivation)
• Instead of simply describing the methods used, look at the methods critically, with an eye for anything interesting or unusual. Point out anything that might be generally useful. For example, did the authors use any techniques that we are currently using in our lab?
• Include graphs and figures from the paper. You can also make your own cartoons and schematic diagrams or show relevant pictures to get across the point.
• Make an effort to explain what is going on in the figures (try to include all of them - but you can leave out some if they do not contribute to a 10 minute presentation)
• Be sure to actually show the images and figures from the paper when talking about them (include some type of caption)
• Do the results suggest any additional experiments that would be the next [[#|step]]?

• Feel [[#|free]] to interject your own viewpoint of the research (is it valuable, did they do anything you liked or disliked?)
• Clearly explain the significance of the results. Results by themselves are dull, unless they have significance. The significance may not be obvious to the audience, so point it out specifically.
  • What is the most significant contribution of the specific [[#|work]] to the field in general?
• Try to appear truly interested (even excited!) about the work you are presenting. Enthusiasm is contagious, and keeps your audience interested. Can you think of anything to make your presentation unique? An unusual prop or visual aid? Make your presentation "professional". That means, stand up in front, look directly at your audience, and don't "read" your slides.
• Go through your talk at least once as a practice run

• TIPS:
  • for [[#|best]] contrast and readability - use black text on white background.
  • Put date on the title slide
  • When you get to a figure, explain what is on the X axis and what is on the Y-axis. This helps them understand the graph and also gives a little time for them to view the graph and digest what is being shown.
  • For graphs and tables - be sure to explicitly state what the 'take home message' of that figure is. What does the graph tell the reader?

Run a draft of your presentation by Dr. B a few days before you present it.
Upload your presentation before class to the GroupMeetingSlides/Journal Club folder on Google Docs

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